Contacts of the strand formed by residues 44 - 49 (chain X) in PDB entry 2AW2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 44 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 6.1 1.2 - - - +
45A GLU 5.8 0.2 - - - -
46A HIS* 5.8 2.7 - - - -
40X ILE* 3.9 10.5 - - - +
41X LYS* 3.1 23.6 + - - -
42X ARG 4.4 0.7 - - - -
43X GLN* 1.3 79.0 - - - +
45X GLU* 1.3 61.4 + - - +
46X HIS* 3.9 10.6 + - - -
128X SER 3.9 3.6 + - - +
129X THR* 2.8 30.8 + - - -
130X THR* 3.1 21.7 + - - -
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Residues in contact with GLU 45 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.4 45.3 + - - +
46A HIS* 3.9 6.5 + - - +
47A SER* 3.2 49.6 + - - +
43X GLN* 3.9 10.3 - - - +
44X SER* 1.3 78.1 + - - +
46X HIS* 1.3 71.2 + - - +
47X SER* 4.8 1.2 + - - -
129X THR* 4.2 0.7 - - - -
130X THR* 3.4 13.0 - - - +
132X TYR* 3.9 26.4 + - + -
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Residues in contact with HIS 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.4 24.5 + - + +
42A ARG 5.3 3.6 - - - -
43A GLN* 4.4 19.0 + - + +
44A SER* 5.9 2.2 - - - -
45A GLU* 3.9 6.1 + - - +
44X SER* 3.9 8.5 + - - -
45X GLU* 1.3 79.3 + - - +
47X SER* 1.3 62.2 - - - +
48X ILE* 4.1 2.1 + - + +
54X PHE* 3.7 29.2 - + + -
55X GLU 6.0 0.4 - - - -
56X LEU* 3.5 24.7 - - + +
129X THR* 3.2 27.2 + - - -
130X THR 3.0 7.0 + - - +
131X LEU* 3.5 12.2 - - + +
132X TYR* 2.9 26.7 + - - +
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Residues in contact with SER 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.2 27.9 + - - +
47A SER* 4.7 8.1 + - - -
132A TYR* 6.4 0.9 - - - -
45X GLU* 4.8 0.7 + - - -
46X HIS* 1.3 72.5 + - - +
48X ILE* 1.3 67.4 + - - +
132X TYR* 3.4 21.7 - - - +
134X THR* 6.4 0.9 - - - -
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Residues in contact with ILE 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X HIS* 4.8 0.9 - - + +
47X SER* 1.3 83.0 - - - +
49X LEU* 1.3 67.2 - - - +
52X ASP* 6.5 0.2 - - + -
54X PHE* 3.5 49.6 - - + -
105X VAL* 3.8 34.8 - - + -
131X LEU* 4.1 17.9 - - + -
132X TYR 3.0 6.4 + - - +
133X VAL* 3.5 21.1 - - + -
134X THR* 3.1 30.7 + - - +
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Residues in contact with LEU 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X ILE* 1.3 78.5 - - - +
50X ALA* 1.3 68.0 + - - +
51X GLY 3.5 1.9 + - - -
52X ASP* 3.5 40.1 + - - +
105X VAL* 4.1 5.5 - - - +
133X VAL* 4.6 2.2 - - - -
134X THR* 3.4 28.0 - - + +
136X VAL* 4.0 18.8 - - + -
138X HIS* 4.0 26.2 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il